One thing to consider is if you have to pass emissions or not. You may need a system where you can replace a a gutted cat or test pipe with a good cat in order to pass emissions, so keep that in mind.
With money not a consideration, I think a lot of people would say a 3" Terry Houston downpipe and the ATR 3' dual stainless steel exhaust are one of the better systems out there for exhaust. I'm not sure what the cat options for the Houston downpipe are, as I have one without a cat and a dump on the GN.
Besides the scan tool, other first mods to consider are an aftermarket boost gauge, an upgraded fuel pump, adjustable fuel pressure regulator and fuel pressure gauge, an adjustable wastegate rod, and a chip. There are some other basic mods you can do that are cheap too. With all of these and some good tires you'll be having fun. Read the spring cleaning and recipes on gnttype.org too.
-murph